OMP ID format

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copied over from the googledoc

https://docs.google.com/document/d/1N3PQM4Prar9aZn5NlJCZJ0rCx7w_G_s2IbIBYXl8CO0/edit#heading=h.whbibz64jbk9

OMP ID Format Prefix Pan-genome: OMP_PG: vs. OMP_PGM vs. ?

Pan-gene: OMP_GN: vs. OMP_PGN vs. ?

Strain/Substrain: OMP_ST: vs. OMP_STR vs. ?

Allele: OMP_AL: vs. OMP_ALL vs. ?

Annotation: OMP_AN: vs. OMP_ANN vs. ?


Jon: Michelle/JH: for Pan-genome TX for taxon or SP for species Number with or without leading zeros? How many zeros? example OMP_GN:000785 vs. OMP_GN:785

No leading zeros

Pangenome:

  • Includes only the genomes of strains.
  • Includes 3 different categories:

1. core genome: genes present in all strains 2. Dispensable genome: genes present in two or more strains 3. Unique genes: specific to single strains


Strains and Sub-strains:

In ecoli wiki the prefix for all strains and their derivatives is “strain:” Should we just omit this prefix in OMP? OMP_ST:00004 ! K-12 vs. OMP_ST:00004 ! Strain:K-12 OMP_ST:00062 ! MG1655 vs. OMP_ST:00062 ! Strain:MG1655

Should we make the distinction between a strain and its derivatives? OMP_ST:00004 ! K-12 OMP_ST:00062 ! K-12_MG1655 vs. OMP_ST:00062 ! MG1655


  • E.coli_K-12_MG1655
  • We will have our own unique ID’s and cross ref with NCBI
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